To investigate the relationship between shallow and intermediate-depth earthquakes and the crust and upper mantle structure beneath the Betic-Cordillera and Alboran sea region, we have applied seismic tomography to 2569 P-wave arrival times from 367 microearthquakes recorded by both permanent and temporary seismic stations deployed in the region. These earthquakes occurred in the depth range of 0 to 110 km beneath the Central Betic Cordilleras and Alboran sea. Our results have revealed significant structural heterogeneities in the crust and upper mantle beneath the study area. In the upper crust there is a high-velocity anomaly at Sierra Gorda (western boundary of the Granada basin) penetrating to 15 km depth, which is in good agreement with the aeromagnetic anomaly. In the Granada basin, a low-velocity anomaly is located in the middle crust, which coincides with a previously detected greater cutoff depth of seismicity, and are considered to be associated with a highly fractured zone generated by an intracrustal detachment. The northern boundary of the Alboran sea (Malaga coast) is well imaged as low velocities from 50 to 90 km depths. This low-velocity zone in the upper mantle is associated with the intermediate-depth seismicity, which outline a section of continental crust related to the collision/subduction beneath the northern part of the Alboran sea-southern part of the Central Betics.